A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
/data/ceph/ssd/scratch/tmp/wayu0/nf-core-drop-result-core4/work/2a/5601ca8e8f48ccd40c3bfb3d1c8fce
Number of samples
Total number of local vs. external samples.
| sample_type | count |
|---|---|
| External | 0 |
| Local | 10 |
Count Quality Control - Mapped vs Counted Reads
Compares total mapped vs counted reads.
The Mapped vs Counted Reads plot does not include external counts.
Consider removing samples with too low or too high size factors.
Count Quality Control - Size Factors
Reads Summary Statistics
| RNA_ID | Reads Mapped | Reads Counted | Size Factors |
|---|---|---|---|
| HG00096 | 62349 | 37088 | 0.9 |
| HG00103 | 58181 | 36655 | 1.0 |
| HG00106 | 63542 | 39291 | 1.0 |
| HG00111 | 77674 | 49223 | 1.2 |
| HG00116 | 61360 | 38422 | 0.9 |
| HG00126 | 72929 | 44651 | 1.1 |
| HG00132 | 79999 | 49977 | 1.2 |
| HG00149 | 66002 | 39384 | 1.0 |
| HG00150 | 71699 | 45629 | 1.1 |
| HG00176 | 60056 | 37036 | 0.8 |
Filtering
Filtering local: A pre-filtered summary of counts using only the local (from BAM) counts. Omitted if no external counts
all: A pre-filtered summary of counts using only the merged local (from BAM) and external counts
passed FPKM: Passes the user defined FPKM cutoff in at least 5% of genes
min 1 read: minimum of 1 read expressed in 5% of genes
min 10 reads: minimum of 10 reads expressed in 5% of genes.
Expressed Genes
Expressed Genes - table
| RNA_ID | Rank | Expressed genes | Union of expressed genes | Intersection of expressed genes | Genes passed filtering |
|---|---|---|---|---|---|
| HG00096 | 3 | 117 | 133 | 99 | 133 |
| HG00103 | 8 | 123 | 157 | 96 | 157 |
| HG00106 | 10 | 125 | 161 | 95 | 161 |
| HG00111 | 7 | 122 | 152 | 97 | 152 |
| HG00116 | 1 | 112 | 112 | 112 | 112 |
| HG00126 | 6 | 120 | 147 | 97 | 147 |
| HG00132 | 4 | 119 | 140 | 98 | 140 |
| HG00149 | 9 | 124 | 159 | 95 | 159 |
| HG00150 | 5 | 119 | 145 | 97 | 145 |
| HG00176 | 2 | 114 | 123 | 103 | 123 |
Sample Sex Annotation
Considerations:The verifying of the samples sex is performed by comparing the expression levels of the genes XIST and UTY. In general, females should have high XIST and low UTY expression, and viceversa for males. For it to work, the sample annotation must have a column called ‘SEX’, with values male/female. If some other values exist, e.g., unknown, they will be matched. The prediction is performed via a linear discriminant analysis on the log2 counts.